Could you try going to Admin -> Manage Installed tool shed repositories
uninstall -> reinstall package_samtools_0_1_18
On 26 November 2014 at 16:55, Anna Terry iseeglass@googlemail.com wrote:
yway, I am also getting the problem with samtools filter sam or bam
I just tried still the same problem. I ran bowtie2 to test, again I saw samtools come up on top, but same error:
Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in finish dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta directly for the initial set_meta call during dataset creation File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, in set_meta raise Exception, "Error Setting BAM Metadata: %s" % stderr Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found
On 26 November 2014 at 16:01, Eric Kuyt eric.kuijt@wur.nl wrote:
Could you try going to Admin -> Manage Installed tool shed repositories
uninstall -> reinstall package_samtools_0_1_18
On 26 November 2014 at 16:55, Anna Terry iseeglass@googlemail.com wrote:
yway, I am also getting the problem with samtools filter sam or bam
-- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad
Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.kuijt@wur.nl Web: http://www.cvi.wur.nl
The problem is that bowtie and Galaxy (can) use a different samtools version. Galaxy needs samtools to create metadata for BAM files, so this process is actually running ofter bowtie has finished. You need a samtools version globally accessible for Galaxy. Make sure you have smatools in your $PATH and than restart Galaxy.
Cheers, Bjoern
2014-11-26 17:14 GMT+01:00 Anna Terry iseeglass@googlemail.com:
I just tried still the same problem. I ran bowtie2 to test, again I saw samtools come up on top, but same error:
Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in finish dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta directly for the initial set_meta call during dataset creation File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, in set_meta raise Exception, "Error Setting BAM Metadata: %s" % stderr Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found
On 26 November 2014 at 16:01, Eric Kuyt eric.kuijt@wur.nl wrote:
Could you try going to Admin -> Manage Installed tool shed repositories
uninstall -> reinstall package_samtools_0_1_18
On 26 November 2014 at 16:55, Anna Terry iseeglass@googlemail.com wrote:
yway, I am also getting the problem with samtools filter sam or bam
-- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad
Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.kuijt@wur.nl Web: http://www.cvi.wur.nl
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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is bash_profile the best place for this, or is somewhere else better?
Cheers Anna
On 26 November 2014 at 16:29, bjoern.gruening@googlemail.com < bjoern.gruening@gmail.com> wrote:
The problem is that bowtie and Galaxy (can) use a different samtools version. Galaxy needs samtools to create metadata for BAM files, so this process is actually running ofter bowtie has finished. You need a samtools version globally accessible for Galaxy. Make sure you have smatools in your $PATH and than restart Galaxy.
Cheers, Bjoern
2014-11-26 17:14 GMT+01:00 Anna Terry iseeglass@googlemail.com:
I just tried still the same problem. I ran bowtie2 to test, again I saw samtools come up on top, but same error:
Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in finish dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta directly for the initial set_meta call during dataset creation File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, in set_meta raise Exception, "Error Setting BAM Metadata: %s" % stderr Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found
On 26 November 2014 at 16:01, Eric Kuyt eric.kuijt@wur.nl wrote:
Could you try going to Admin -> Manage Installed tool shed repositories
uninstall -> reinstall package_samtools_0_1_18
On 26 November 2014 at 16:55, Anna Terry iseeglass@googlemail.com wrote:
yway, I am also getting the problem with samtools filter sam or bam
-- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad
Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.kuijt@wur.nl Web: http://www.cvi.wur.nl
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
I would use .bashrc. You can also try to symlib the default dir to the actual /bin directory. Maybe this works for you.
2014-11-26 17:36 GMT+01:00 Anna Terry iseeglass@googlemail.com:
is bash_profile the best place for this, or is somewhere else better?
Cheers Anna
On 26 November 2014 at 16:29, bjoern.gruening@googlemail.com < bjoern.gruening@gmail.com> wrote:
The problem is that bowtie and Galaxy (can) use a different samtools version. Galaxy needs samtools to create metadata for BAM files, so this process is actually running ofter bowtie has finished. You need a samtools version globally accessible for Galaxy. Make sure you have smatools in your $PATH and than restart Galaxy.
Cheers, Bjoern
2014-11-26 17:14 GMT+01:00 Anna Terry iseeglass@googlemail.com:
I just tried still the same problem. I ran bowtie2 to test, again I saw samtools come up on top, but same error:
Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in finish dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta directly for the initial set_meta call during dataset creation File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, in set_meta raise Exception, "Error Setting BAM Metadata: %s" % stderr Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found
On 26 November 2014 at 16:01, Eric Kuyt eric.kuijt@wur.nl wrote:
Could you try going to Admin -> Manage Installed tool shed repositories
uninstall -> reinstall package_samtools_0_1_18
On 26 November 2014 at 16:55, Anna Terry iseeglass@googlemail.com wrote:
yway, I am also getting the problem with samtools filter sam or bam
-- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad
Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.kuijt@wur.nl Web: http://www.cvi.wur.nl
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
great, thanks
On 26 November 2014 at 16:39, bjoern.gruening@googlemail.com < bjoern.gruening@gmail.com> wrote:
I would use .bashrc. You can also try to symlib the default dir to the actual /bin directory. Maybe this works for you.
2014-11-26 17:36 GMT+01:00 Anna Terry iseeglass@googlemail.com:
is bash_profile the best place for this, or is somewhere else better?
Cheers Anna
On 26 November 2014 at 16:29, bjoern.gruening@googlemail.com < bjoern.gruening@gmail.com> wrote:
The problem is that bowtie and Galaxy (can) use a different samtools version. Galaxy needs samtools to create metadata for BAM files, so this process is actually running ofter bowtie has finished. You need a samtools version globally accessible for Galaxy. Make sure you have smatools in your $PATH and than restart Galaxy.
Cheers, Bjoern
2014-11-26 17:14 GMT+01:00 Anna Terry iseeglass@googlemail.com:
I just tried still the same problem. I ran bowtie2 to test, again I saw samtools come up on top, but same error:
Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in finish dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta directly for the initial set_meta call during dataset creation File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, in set_meta raise Exception, "Error Setting BAM Metadata: %s" % stderr Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found
On 26 November 2014 at 16:01, Eric Kuyt eric.kuijt@wur.nl wrote:
Could you try going to Admin -> Manage Installed tool shed repositories
uninstall -> reinstall package_samtools_0_1_18
On 26 November 2014 at 16:55, Anna Terry iseeglass@googlemail.com wrote:
yway, I am also getting the problem with samtools filter sam or bam
-- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad
Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.kuijt@wur.nl Web: http://www.cvi.wur.nl
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
galaxy-dev@lists.galaxyproject.org
-
Anna Terry -
bjoern.gruening＠googlemail.com -
Eric Kuyt